Transcription factor Rel regulates the transcription of effector genes involved in immune response by cooperating with IκBs in lamprey (Lethenteron reissneri) DOI Creative Commons

Yang Cai,

Xinyu Du,

Jessica Aijia Liu

et al.

The Journal of Immunology, Journal Year: 2025, Volume and Issue: unknown

Published: March 12, 2025

Abstract The Rels, a class of nuclear factor κB (NF-κB) complexes, regulate diverse physiological processes by modulating the transcription effector genes. IκBs are critical proteins that inhibit NF-κB translocation, thereby disrupting NF-κB-mediated signaling pathways. Despite this, precise role and underlying molecular mechanisms Rel IκB transcriptional regulation mediated in lamprey, member oldest surviving vertebrates, remain incompletely understood. In this study, we cloned identified 4 Rels (designated Lr_Rels) Lr_IκBs) from lamprey explored their sequence structures evolutionary process, indicating Lr_Rels Lr_IκBs represent ancestral lineages dimerization domain (DD) might be crucial for Lr_Rels’ function. Immunoreactivity assays demonstrated significant induction Lr_Rel1 expression across various tissues following LPS polyinosinic–polycytidylic acid (poly (I:C)) challenge. Functional characterization revealed mediates through translocation sequence-specific recognition, with its activity being inhibited Lr_IκBs. Furthermore, homology region (RHR) activation (TAD) were as key elements Thirteen target genes also identified, each containing conserved κB-binding sites within promoter regions. Our study cooperation between Lr_Rel Lr_IκBs, providing insights into protein immune pathway.

Language: Английский

Transcription activation is enhanced by multivalent interactions independent of phase separation DOI Creative Commons
Jorge Trojanowski, Lukas Frank, Anne Rademacher

et al.

Molecular Cell, Journal Year: 2022, Volume and Issue: 82(10), P. 1878 - 1893.e10

Published: May 1, 2022

Language: Английский

Citations

168
Plant transcription factors — being in the right place with the right company DOI Creative Commons
Lucia C. Strader, Dolf Weijers, Doris Wagner

et al.

Current Opinion in Plant Biology, Journal Year: 2021, Volume and Issue: 65, P. 102136 - 102136

Published: Nov. 29, 2021

Language: Английский

Citations

128
Liquid–Liquid Phase Separation in Chromatin DOI Open Access
Karsten Rippe

Cold Spring Harbor Perspectives in Biology, Journal Year: 2021, Volume and Issue: 14(2), P. a040683 - a040683

Published: June 14, 2021

Karsten Rippe Division of Chromatin Networks, German Cancer Research Center (DKFZ) and Bioquant, 69120 Heidelberg, Germany Correspondence: Karsten.Rippe{at}dkfz.de

Language: Английский

Citations

110
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes DOI Creative Commons
Sandipan Brahma, Steven Henikoff

Nature Genetics, Journal Year: 2023, Volume and Issue: 56(1), P. 100 - 111

Published: Dec. 4, 2023

Abstract Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, remodeling chromatin are unclear. Here, we used chemical–genetic approach coupled with time-resolved profiling to dissect interplay RNA Polymerase II (RNAPII), BAF DNA-sequence-specific factors in mouse embryonic stem cells. We show that dynamically unwraps evicts nucleosomes at accessible regions, while RNAPII promoter-proximal pausing stabilizes occupancy enhances eviction BAF. find although probe both transcriptionally Polycomb-repressed genomic pluripotency binding confers locus specificity for productive Our study suggests paradigm how functional synergy acting regulates locus-specific organization accessibility.

Language: Английский

Citations

43
Transcription factor exchange enables prolonged transcriptional bursts DOI Creative Commons
Wim Pomp, Joseph V.W. Meeussen, Tineke L. Lenstra

et al.

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(6), P. 1036 - 1048.e9

Published: Feb. 19, 2024

Language: Английский

Citations

28
Genome-Wide Identification and Analysis of bZIP Gene Family and Resistance of TaABI5 (TabZIP96) under Freezing Stress in Wheat (Triticum aestivum) DOI Open Access
Yi Liang,

Jing‐Qiu Xia,

Yunshuang Jiang

et al.

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(4), P. 2351 - 2351

Published: Feb. 21, 2022

The basic leucine zipper (bZIP) regulates plant growth and responds to stress as a key transcription factor of the Abscisic acid (ABA) signaling pathway. In this study, TabZIP genes were identified in wheat gene structure, physicochemical properties, cis-acting elements, collinearity analyzed. RNA-Seq qRT-PCR analysis showed that ABA abiotic induced most expression. ectopic expression TaABI5 up-regulated several cold-responsive Arabidopsis. Physiological indexes seedlings different lines under freezing enhanced tolerance plants. Subcellular localization is localized nucleus. Furthermore, physically interacted with cold-resistant TaICE1 yeast two-hybrid system. conclusion, study analyzed members family wheat. It proved for first time affected cold transgenic plants was convenient us understand resistance molecular mechanism TaABI5. These results will provide new inspiration further on improving resistance.

Language: Английский

Citations

50
Following the tracks: How transcription factor binding dynamics control transcription DOI Creative Commons

Wim J. de Jonge,

Heta Patel, Joseph V.W. Meeussen

et al.

Biophysical Journal, Journal Year: 2022, Volume and Issue: 121(9), P. 1583 - 1592

Published: March 23, 2022

Transcription, the process of copying genetic information from DNA to messenger RNA, is regulated by sequence-specific DNA-binding proteins known as transcription factors (TFs). Recent advances in single-molecule tracking (SMT) technologies have enabled visualization individual TF molecules they diffuse and interact with context living cells. These SMT studies uncovered multiple populations events characterized their distinctive residence times. In this perspective, we review recent insights into how these times relate specific non-specific binding, well contribution domains on dynamics. We discuss different models that aim link transient binding TFs bursts present an outlook for future microscopy development may broaden our understanding dynamics molecular steps underlie activation.

Language: Английский

Citations

40
Single-molecule tracking (SMT): a window into live-cell transcription biochemistry DOI Creative Commons
Liza Dahal, Nike Walther, Robert Tjian

et al.

Biochemical Society Transactions, Journal Year: 2023, Volume and Issue: 51(2), P. 557 - 569

Published: March 6, 2023

How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as case study, we describe SMT works, what it can tell us about molecular biology, and has changed our perspective on inner workings nucleus. We also cannot yet new technical advances seek to overcome its limitations. This ongoing progress will be imperative address outstanding questions machines function in

Language: Английский

Citations

29
Chromatin organization drives the search mechanism of nuclear factors DOI Creative Commons
Matteo Mazzocca, Alessia Loffreda,

Emanuele Colombo

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Oct. 13, 2023

Nuclear factors rapidly scan the genome for their targets, but role of nuclear organization in such search is uncharted. Here we analyzed how multiple explore chromatin, combining live-cell single-molecule tracking with multifocal structured illumination DNA density. We find that displaying higher bound fractions sample DNA-dense regions more exhaustively. Focusing on tumor-suppressor p53, demonstrate it searches targets by alternating between rapid diffusion interchromatin compartment and compact sampling chromatin dense regions. Efficient targeting requires balanced interactions chromatin: fusing p53 an exogenous intrinsically disordered region potentiates p53-mediated target gene activation at low concentrations, leads to condensates levels, derailing its downregulating transcription. Our findings highlight showcase a powerful method generate traffic maps eukaryotic nucleus dissect guides action.

Language: Английский

Citations

28
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription DOI Creative Commons
Kathleen S Metz Reed, Eric S. Davis, Marielle L. Bond

et al.

Cell Reports, Journal Year: 2022, Volume and Issue: 41(5), P. 111567 - 111567

Published: Nov. 1, 2022

To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly spaced time points of macrophage activation. Enhancers genes connected by loops exhibit stronger correlations histone H3K27 acetylation expression than can be explained genomic distance or physical proximity alone. At these looped enhancer-promoter pairs, changes at distal enhancers precede expression. Changes directional bias differential loop anchors; gained are associated with increased oriented away from the center loop, lost often accompanied high levels transcription within boundaries themselves. These results consistent reciprocal relationship where facilitate connecting promoters to whereas impede formation.

Language: Английский

Citations

34